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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatatgtgggttttaaactctcaaatgctattaattgacatagtttgacattagtgattagccctggtttttaataaaatgaaaatgctcttgctaacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG

Basic information

species Glycine max
transcript GLYMA14G00760.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G00760.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 9
-aatatgtgggttttaaactctcaaatgctattaattgacatagtttgacatt-agtgatta-gccctggtttttaataaaatgaaaatgctcttgctaacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG
     |||   | |  || |      |   ||     ||  |  ||    ||  |||||    |   || || |||   || |     | |       |||||||| |||||||| ||| |||| |||||||||||  |||||||||   | ||||| || ||||||||||||  |||||  |||| ||| ||||| ||||| 
ttgactgttcttatccaattggtgcgtaaaatccccagatgtgtttgtttatccagtgagagtgtgatgcttcttagctaatttgttttacatgg---aacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA

upper sequence: GLYMA14G00760.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 7
aatatgtgggttttaaactctcaaatgctattaattgacatagtttgacattagtgattagcc--ctggtttttaataaaatgaaaatgctcttgctaa--cagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG
    |||   |||| | ||  | | | || |  | ||   ||  |     |   ||  |||||  ||| |      || |    |  |||| |   |    ||||||||| ||||||||| ||| ||||||||||||  ||||||| |   ||||||| || |||||  ||||||  ||||  |||||||||||||| ||||| 
----tgtctatttttagctgaccagtactgtccagtgtactaactactattgcttgtctagccttctgctaccacttatatctgatttgctttatatcgttcagTGATGGAGCTGCTGCATTAGCTTTGGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTGCAAGTCCTTGCAAGGATCAAAGGATATGCTGATGCAGCTCAA

upper sequence: GLYMA14G00760.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 9
aatatgtgggttttaaactctcaaatgctattaattgacatagtttgacattagtgat-tagccctggtttttaataaaatgaaaatgctcttgct--aacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG
  | |||   |||| | ||  ||| | || |    ||  |  |  |   ||   |  | ||||| |        |   |   ||  || | |   |  | ||||||||| ||||||||| ||||||| ||||||||  ||||||| |   ||||||| ||||||||  ||||||  ||||  || ||||||||||| ||||| 
--tgtgtctatttttagctgacaagtactgtccggtg-tactgcctactatggcttgtgtagccttctgcaaccagtcatctaatttgttttatatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA

upper sequence: GLYMA14G00760.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 9
aatatgtgggttttaaactctcaaatgctattaattg-acatagtttgacattagtgat-tagccctggtttttaataaaatgaaaatgctcttgct---aacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG
  |   |   ||||  | |  |   | |  || | ||   |  |  |   | |  || | ||||     |   | |||      |  |||| ||      | ||||||||| || |||||| ||||||||||||||||  ||||||| |   ||||||| || |||||  ||||||  ||||  |||||||| ||||| ||||| 
--tgc-tattttttccattggctggtaccgttcagtgtgtactgcctactactgctggtgtagctacaatcggtcatat--ctgatttgcttttatatggatcagTGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTGCAAGTCCTTGCAAGGATCAGAGGATATGCAGATGCGGCTCAA

upper sequence: GLYMA14G00760.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 9
aatatgtgggttttaaactctcaa--atgctattaattgacatagtttgacattagtgattagc-cctggtttttaataaaatgaaaatgctcttgctaacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG
   |  |    ||  || |   ||  || | ||| |   |  | | |||||||   |  |      |||  || || | ||| |  ||    ||     |||||||||||||||||||  |||||||||| |||||||||||||||||  | ||||||||   ||| ||||| || ||  | ||||| |||||||||||||||
---aattaaaattgtaattgaaaatgattccatttaagtatgtgggttgacatccattttggttatctgtcttatactgaaaagtgaaattgctcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACTTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|15812294|gb|BI784569.1|BI784569
EST:     TTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAG                         TGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCT
genomic: TTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAGgttaatatat ... ttgctaacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCT
EST: gi|298184901|gb|HO030114.1|HO030114
EST:     AAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAG                         TGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCT
genomic: AAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAGgttaatatat ... ttgctaacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCT
EST: gi|192328380|gb|FK020091.1|FK020091
EST:     TTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAG                         TGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCT
genomic: TTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAGgttaatatat ... ttgctaacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCT
EST: gi|209708680|gb|BW678861.1|BW678861
EST:     TTCAAGGAGACTGGAGGTTCTGTTACTGCTGGCAATGCTTCCAGCATAAG                         TGATGGTGCCGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCT
genomic: TTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAGgttaatatat ... ttgctaacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCT
EST: gi|37994372|gb|CF806118.1|CF806118
EST:     TTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAG                         TGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCT
genomic: TTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAGgttaatatat ... ttgctaacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacattagtgattagccctggtttttaataaaatgaaaatgctcttgctaacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG
                       ttttaat  putative branch site (score: 3)
                                          ctcttgct  putative PPT
                   tggtttttaataaaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatatgtgggttttaaactctcaaatgctattaattgacatagtttgacattagtgattagccctggtttttaataaaatgaaaatgctcttgctaacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - tgtgggt
- - - - - - - - - - -caaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgctc